000163821 001__ 163821
000163821 005__ 20251107115328.0
000163821 0247_ $$2doi$$a10.1186/s13007-025-01458-6
000163821 0248_ $$2sideral$$a145975
000163821 037__ $$aART-2025-145975
000163821 041__ $$aeng
000163821 100__ $$aSancho, R.
000163821 245__ $$aAlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids
000163821 260__ $$c2025
000163821 5060_ $$aAccess copy available to the general public$$fUnrestricted
000163821 5203_ $$aBackground: The genomic and evolutionary study of allopolyploid organisms involves multiple copies of homeologous chromosomes, making their assembly, annotation, and phylogenetic analysis challenging. Bioinformatics tools and protocols have been developed to study polyploid genomes, but sometimes require the assembly of their genomes, or at least the genes, limiting their use.
Results: We have developed AlloSHP, a command-line tool for detecting and extracting single homeologous polymorphisms (SHPs) from the subgenomes of allopolyploid species. This tool integrates three main algorithms, WGA, VCF2ALIGNMENT and VCF2SYNTENY, and allows the detection of SHPs for the study of diploid-polyploid complexes with available diploid progenitor genomes, without assembling and annotating the genomes of the allopolyploids under study. AlloSHP has been validated on three diploid-polyploid plant complexes, Brachypodium, Brassica, and Triticum-Aegilops, and a set of synthetic hybrid yeasts and their progenitors of the genus Saccharomyces. The results and congruent phylogenies obtained from the four datasets demonstrate the potential of AlloSHP for the evolutionary analysis of allopolyploids with a wide range of ploidy and genome sizes.
Conclusions: AlloSHP combines the strategies of simultaneous mapping against multiple reference genomes and syntenic alignment of these genomes to call SHPs, using as input data a single VCF file and the reference genomes of the known or closest extant diploid progenitor species. This novel approach provides a valuable tool for the evolutionary study of allopolyploid species, both at the interspecific and intraspecific levels, allowing the simultaneous analysis of a large number of accessions and avoiding the complex process of assembling polyploid genomes.
000163821 536__ $$9info:eu-repo/grantAgreement/ES/DGA/A08-20R$$9info:eu-repo/grantAgreement/ES/DGA-FSE/A01-17R$$9info:eu-repo/grantAgreement/ES/DGA-FSE/A01-20R$$9info:eu-repo/grantAgreement/ES/DGA-FSE/A01-23R$$9info:eu-repo/grantAgreement/ES/MICINN/PID2019-108195GB-I00$$9info:eu-repo/grantAgreement/ES/MICINN/PID2022-140074NB-I00$$9info:eu-repo/grantAgreement/ES/MINECO/AGL2013-48756-R$$9info:eu-repo/grantAgreement/ES/MICINN/BES-2013-066228$$9info:eu-repo/grantAgreement/ES/MINECO/CGL2016-79790-P$$9info:eu-repo/grantAgreement/ES/MINECO/EEBB-I-15-09760$$9info:eu-repo/grantAgreement/ES/UZ/UZ2016-TEC-02
000163821 540__ $$9info:eu-repo/semantics/openAccess$$aby-nc-nd$$uhttps://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
000163821 655_4 $$ainfo:eu-repo/semantics/article$$vinfo:eu-repo/semantics/publishedVersion
000163821 700__ $$aCatalán, P.
000163821 700__ $$aVogel, J. P.
000163821 700__ $$0(orcid)0000-0002-5462-907X$$aContreras-Moreira, B.
000163821 773__ $$g21, 1 (2025), [19 pp.]$$pPlant Methods$$tPlant Methods$$x1746-4811
000163821 8564_ $$s2159477$$uhttps://zaguan.unizar.es/record/163821/files/texto_completo.pdf$$yVersión publicada
000163821 8564_ $$s2228358$$uhttps://zaguan.unizar.es/record/163821/files/texto_completo.jpg?subformat=icon$$xicon$$yVersión publicada
000163821 909CO $$ooai:zaguan.unizar.es:163821$$particulos$$pdriver
000163821 951__ $$a2025-11-07-10:25:23
000163821 980__ $$aARTICLE